Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2570
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 75576
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1333 original size:68 final size:68
Alignment explanation
Indices: 1239--1396 Score: 298
Period size: 68 Copynumber: 2.3 Consensus size: 68
1229 TTTACTTGGA
* *
1239 ATCACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1304 CGT
66 CGT
1307 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1372 CGT
66 CGT
1375 ATCACACATGTGACCTAGCTAC
1 ATCACACATGTGACCTAGCTAC
1397 TATATAGTAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 88 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (68 bp):
ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
CGT
Found at i:2730 original size:39 final size:39
Alignment explanation
Indices: 2676--2853 Score: 252
Period size: 39 Copynumber: 4.5 Consensus size: 39
2666 TAATGGAGAA
*
2676 TTATATCCGGGCTAAGTCCCGAAGGTATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
2715 TTATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
2754 TTATATCTGGGCTAAGT-CCGAAGGCATTCGTGCTAGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
2792 TTATATCCGGGCTAAAGTCCCGTAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
2831 TTATATCCGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
2854 CATGCTTTGT
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
38 31 0.25
39 78 0.62
40 17 0.13
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:2804 original size:77 final size:78
Alignment explanation
Indices: 2675--2853 Score: 254
Period size: 77 Copynumber: 2.3 Consensus size: 78
2665 ATAATGGAGA
* *
2675 ATTATATCCGGGCTAAGTCCCGAAGGTATTCGTGCTGGTGTTATATCCGGGCT-AAGTCCCAAAG
1 ATTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTGTTATATCCGGGCTAAAGTCCCAAAG
2739 GCATTCGTGCTGGT
66 GC-TTCGTGCTGGT
* * **
2753 GTTATATCTGGGCTAAGT-CCGAAGGCATTCGTGCTAGTGTTATATCCGGGCTAAAGTCCCGTAG
1 ATTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTGTTATATCCGGGCTAAAGTCCCAAAG
*
2817 GCTTTGTGCTGGT
66 GCTTCGTGCTGGT
2830 ATTATATCCGGGCTTAAAGTCCCG
1 ATTATATCCGGGC-T-AAGTCCCG
2854 CATGCTTTGT
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
77 53 0.60
78 28 0.32
79 4 0.05
80 3 0.03
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (78 bp):
ATTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTAGTGTTATATCCGGGCTAAAGTCCCAAAG
GCTTCGTGCTGGT
Found at i:10622 original size:28 final size:28
Alignment explanation
Indices: 10591--10674 Score: 150
Period size: 28 Copynumber: 3.0 Consensus size: 28
10581 CTCTTTCATA
10591 TGGCCCATTAGGCCCATTCACATTTACG
1 TGGCCCATTAGGCCCATTCACATTTACG
10619 TGGCCCATTAGGCCCATTCACATTTACG
1 TGGCCCATTAGGCCCATTCACATTTACG
*
10647 TGGCCCATTAGGCCCAAATCACATTTAC
1 TGGCCCATTAGGCCC-ATTCACATTTAC
10675 AGTCATGCTC
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 43 0.80
29 11 0.20
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
TGGCCCATTAGGCCCATTCACATTTACG
Found at i:10632 original size:56 final size:56
Alignment explanation
Indices: 10564--10674 Score: 127
Period size: 56 Copynumber: 2.0 Consensus size: 56
10554 TACCTATATA
* * * *
10564 TGGCCCACAGGCCTAATCTC-TTTCATATGGCCCATTAGGCCC-ATTCACATTTACG
1 TGGCCCACAGGCCCAATCACATTT-ACATGGCCCATTAGGCCCAAATCACATTTACG
* * *
10619 TGGCCCATTAGGCCCATTCACATTTACGTGGCCCATTAGGCCCAAATCACATTTAC
1 TGGCCCA-CAGGCCCAATCACATTTACATGGCCCATTAGGCCCAAATCACATTTAC
10675 AGTCATGCTC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
55 7 0.15
56 25 0.54
57 14 0.30
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.28
Consensus pattern (56 bp):
TGGCCCACAGGCCCAATCACATTTACATGGCCCATTAGGCCCAAATCACATTTACG
Found at i:10920 original size:16 final size:16
Alignment explanation
Indices: 10899--10935 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
10889 TCAGCTTTTT
10899 CATTTCGACTTTTCGG
1 CATTTCGACTTTTCGG
*
10915 CATTTCGGCTTTTCGG
1 CATTTCGACTTTTCGG
*
10931 GATTT
1 CATTT
10936 GCCGATTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (16 bp):
CATTTCGACTTTTCGG
Found at i:19004 original size:46 final size:46
Alignment explanation
Indices: 18917--19089 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 46
18907 GTATCCATGT
*
18917 CGATGCCATGTCCCAGACATGGTCTTACACTGACATGTCTCGTA-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCATGTCTCG-AGGC
*
18963 TGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTATGTCTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGC--ATGTCTCGAGGC
* * * * * *
19009 CAATG-CATGCCCCGGACAT-GTCTTACACTAGCACTCGTCTCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCA-T-GTCTCGAGGC
19055 CGATGCCATGTCCCAGACATGGTCTTACACTGGCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCA
19090 CACAAATTAC
Statistics
Matches: 107, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
44 13 0.12
45 16 0.15
46 53 0.50
47 12 0.11
48 13 0.12
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (46 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCATGTCTCGAGGC
Found at i:25264 original size:13 final size:13
Alignment explanation
Indices: 25248--25272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25238 TGGACACACA
25248 CCCGTGTCCTTTG
1 CCCGTGTCCTTTG
25261 CCCGTGTCCTTT
1 CCCGTGTCCTTT
25273 CACACGGCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.40, G:0.20, T:0.40
Consensus pattern (13 bp):
CCCGTGTCCTTTG
Found at i:37505 original size:20 final size:20
Alignment explanation
Indices: 37461--37506 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
37451 AATTTGTTAA
*
37461 AGGTGGTTTCAGTTTTGGAAG
1 AGGTGGTTTCAATTTT-GAAG
37482 -GGTGGTTTCAATTTT-AAG
1 AGGTGGTTTCAATTTTGAAG
37500 CAGGTGG
1 -AGGTGG
37507 GTGAGTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 3 0.14
20 19 0.86
ACGTcount: A:0.20, C:0.07, G:0.37, T:0.37
Consensus pattern (20 bp):
AGGTGGTTTCAATTTTGAAG
Found at i:46970 original size:13 final size:13
Alignment explanation
Indices: 46952--46976 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46942 CTCGGCAGGG
46952 ACATGCCCGTGTA
1 ACATGCCCGTGTA
46965 ACATGCCCGTGT
1 ACATGCCCGTGT
46977 GCGATTACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.24
Consensus pattern (13 bp):
ACATGCCCGTGTA
Found at i:52332 original size:18 final size:19
Alignment explanation
Indices: 52309--52352 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
52299 AACAAAGTTG
52309 GGGGAAAGGAA-GAAGAAA
1 GGGGAAAGGAAGGAAGAAA
52327 GGGG-AA-GAAGGGAAGAAA
1 GGGGAAAGGAA-GGAAGAAA
52345 -GGGAAAGG
1 GGGGAAAGG
52353 GGATTGGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
16 3 0.14
17 5 0.23
18 13 0.59
19 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (19 bp):
GGGGAAAGGAAGGAAGAAA
Found at i:63210 original size:40 final size:39
Alignment explanation
Indices: 63114--63231 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 39
63104 ATAATGGAGA
* *
63114 ATTATATCCGGGCT-AAGTCCCAAAGGCATTCGTGCTGGT
1 ATTATATCCGGGCTAAAGTCCCGAAGGC-TTTGTGCTGGT
* * * *
63153 GTTATATCTGGGCTAAAGTCCCGTAGGCTTTGTGTTGGT
1 ATTATATCCGGGCTAAAGTCCCGAAGGCTTTGTGCTGGT
* * * *
63192 ATTATATCCGGGCTTAAAGTCCTGCATGCTTTGTGGTGGT
1 ATTATATCCGGGC-TAAAGTCCCGAAGGCTTTGTGCTGGT
63232 GATTGGATTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
39 32 0.49
40 33 0.51
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (39 bp):
ATTATATCCGGGCTAAAGTCCCGAAGGCTTTGTGCTGGT
Found at i:64271 original size:39 final size:40
Alignment explanation
Indices: 64227--64313 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
64217 TTGCTAAATA
** *
64227 TGCTGGTGTTATATCCGGGC-TAAAGTCCCATAGGCTTTG
1 TGCTGGTGTTATATCAAGGCTTAAAGTCCCACAGGCTTTG
* * *
64266 TGCTGGTATTATATCAAGGCTTAAAGTCCCGCATGCTTTG
1 TGCTGGTGTTATATCAAGGCTTAAAGTCCCACAGGCTTTG
*
64306 TGGTGGTG
1 TGCTGGTG
64314 ATTGGATTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
39 17 0.44
40 22 0.56
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.34
Consensus pattern (40 bp):
TGCTGGTGTTATATCAAGGCTTAAAGTCCCACAGGCTTTG
Found at i:70110 original size:40 final size:39
Alignment explanation
Indices: 69844--70083 Score: 394
Period size: 39 Copynumber: 6.2 Consensus size: 39
69834 TAATGGAGAA
69844 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
69883 TTGTATCC-GGCTAAGTCCCGAAGGCATTCATGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
69921 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
69960 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
69999 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
70038 TTATATCCGGGCTAAAGTCCCGTAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
70077 TTATATC
1 TTATATC
70084 AAGGCTTAAA
Statistics
Matches: 188, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
38 35 0.19
39 141 0.75
40 12 0.06
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Done.